bb.test {ibb} | R Documentation |
Performs the beta-binomial test for count data.
bb.test(x, tx, group, alternative = c("two.sided", "less", "greater"), n.threads = 1)
x |
A vector or matrix of counts. When |
tx |
A vector or matrix of the total sample counts. When |
group |
A vector of group indicators. |
alternative |
A character string specifying the alternative hypothesis: "two.sided" (default), "greater" or "less". |
n.threads |
The number of threads to be used. |
When n.threads
is 0, the maximal number of CPU cores is used. When n.threads
is -1, one CPU core less than the maximum is used, and so on.
A list with a single component is returned:
p.value |
The p-value of the test. |
Thang V. Pham
Pham TV, Piersma SR, Warmoes M, Jimenez CR (2010) On the beta binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics, 26(3):363-369.
x <- c(1, 5, 1, 10, 9, 11, 2, 8) tx <- c(19609, 19053, 19235, 19374, 18868, 19018, 18844, 19271) group <- c(rep("cancer", 3), rep("normal", 5)) bb.test(x, tx, group)